Welcome to the Procooling forms!
(hehe beat BigBen for once

)
You should fill your entire system with water but leave a small air gap in your res. Your res. should be the only place where there is any air in your system.
If you are having specific problems with your system and noise, you might have something configured slightly out of place.
First of all:
How do you have your water system setup? AKA positioning of your components; be specific.
Is your res. the highest part of your system?
Do you have all 1/2" tubing or 3/8" tubing?
Do you use a additive in your water like WaterWetter?
Those details will help us out a lot when trying to figure out why your system is now noisy.